I have the same model and it took me a few tries to really understand the best way to set up the door.
What I do now is raise the roof to the height I want, go in and lower the door, then go outside. With the lower door closed, I position the upper part over the lower, get the pegs line up at the bottom. At this point you can see if the trailer is level front to back by observing the top part of the bottom compared to the bottom part of the top... level as necessary. Once that's done, I stand on the step and slip my hands inside the canvas at the metal plate at the top of the door.. I then gently pull the plate forward so it slides over the locks. It should pop into place easily, if not, make sure you don't have any curtains behind the plate, or canvas between the plate and door frame. If it's still too tight, raise the roof a skosh.. 1/8 turn increments. If it pops into place really easy, you can lower the roof a bit.
The roof height is correct when the upper door channel overlaps the bottom door by some, but not too much.
1995 Toyota 4Runner SR5 4WD 5 spd
2002 Eagle Summit 12